Unlinking of Supercoiled DNA Catenanes by Type IIA Topoisomerases Alexander Vologodskii  Biophysical Journal  Volume 101, Issue 6, Pages 1403-1411 (September 2011) DOI: 10.1016/j.bpj.2011.08.011 Copyright © 2011 Biophysical Society Terms and Conditions

Figure 1 Regular form of a torus catenane. The linking number of the two contours, Ca, equals 7. Each contour of the catenane forms a right-handed helix in this conformation, with a positive Wr. In this particular conformation, Wr of each contour equals 1.22. Biophysical Journal 2011 101, 1403-1411DOI: (10.1016/j.bpj.2011.08.011) Copyright © 2011 Biophysical Society Terms and Conditions

Figure 2 Diagram of simple (left) and interwound helices (right) closed by loops. Although the writhe of the helices depends on the winding angles α, it is always positive for a right-handed simple helix and negative for a right-handed interwound helix (20). Biophysical Journal 2011 101, 1403-1411DOI: (10.1016/j.bpj.2011.08.011) Copyright © 2011 Biophysical Society Terms and Conditions

Figure 3 Typical simulated conformations of supercoiled DNA catenanes. The simulations correspond to DNA molecules of 2.9 kb in length and Ca of 11 (A) and 5 (B). The values of σ, shown near each of the conformations, are identical for each of the model chains. Biophysical Journal 2011 101, 1403-1411DOI: (10.1016/j.bpj.2011.08.011) Copyright © 2011 Biophysical Society Terms and Conditions

Figure 4 Juxtaposition of DNA segments in the replication catenanes. The computation was performed for two values of ς, 0.08 (open circles) and 0.036 (solid circles). The effective concentration of one segment in the vicinity of another segment was calculated for interchain (solid lines and symbols) and intrachain juxtapositions (shaded lines and symbols). The computation was performed for DNA molecules of 2.9 kb in length. Biophysical Journal 2011 101, 1403-1411DOI: (10.1016/j.bpj.2011.08.011) Copyright © 2011 Biophysical Society Terms and Conditions

Figure 5 Definition of the angle between two juxtaposed DNA segments. If the segments have a directionality, the angle is specified in interval [0, 360°]. The directionality, specified by the segment sequence or by the connectivity of the DNA contour, cannot be essential for proteins that bind DNA without sequence specificity. In this case, the interval of distinguishable angles is reduced to [0, 180°], as the figure shows. Biophysical Journal 2011 101, 1403-1411DOI: (10.1016/j.bpj.2011.08.011) Copyright © 2011 Biophysical Society Terms and Conditions

Figure 6 Distributions of angles between juxtaposed segments in supercoiled torus catenanes. The distributions for interchain (solid lines and symbols) and intrachain (shaded lines and symbols) juxtapositions were obtained via the statistical analysis of simulated equilibrium sets of catenane conformations. The computation was performed for ς of 0.08 (A) and for ς of 0.036 (B). For comparison, the angle distribution for two random vectors uniformly distributed in space (A, top panel) is shown (dotted line). Biophysical Journal 2011 101, 1403-1411DOI: (10.1016/j.bpj.2011.08.011) Copyright © 2011 Biophysical Society Terms and Conditions

Figure 7 Typical conformations of supercoiled replication catenanes with the bent protein-bound G-segment (shown by red (dark)). In loose conformations of (+) supercoiled catenanes (A), segments of the other chain are often located in the interior of the G-segment, so they can serve as T-segments. In the (−) supercoiled catenanes (B), strongly bent G-segments are nearly always located at one of the branch apices. In this case, the interior of the G-segment is hardly accessible to other segments of the chains. Biophysical Journal 2011 101, 1403-1411DOI: (10.1016/j.bpj.2011.08.011) Copyright © 2011 Biophysical Society Terms and Conditions